An integrated geophysical and hydrogeological study is carried out on the San Luis Potosí aquifer system and a transient flow model and are proposed alternative exploitation scenarios. The aquifer water balance between recharge and extraction indicates a deficit of 100 Hm3 by the year 2005. A comparison of the historical potentiometric levels recorded between 1972 and 2005 shows a cone of depression 80 m deep extending over an area of 70 km2 inside of San Luis Potosí City. The model suggests that the aquifer is sensitive to the locations of extraction wells. Predictive models are developed and remediation measures are proposed as alternatives to current extraction procedures in order for the aquifer system to recover.